From early Egyptian times the island was sacred to the goddess Isis; the earliest structures known are those of Taharqa (reigned 690–664 BC), the Cushite 25th-dynasty pharaoh. The Saites (664–525 BC) built the earliest-known temple, found dismantled and reused in the Ptolemaic structures. Nectanebo II (Nekhtharehbe 【reigned 360–343 BC】), last pharaoh of the 30th dynasty and last independent native ruler of Egypt prior to 1952, added the present colonnade. The complex of structures of the Temple of Isis was completed by Ptolemy II Philadelphus (reigned 285–246 BC) and his successor, Ptolemy III Euergetes (fl. 246–221 BC). Its decorations, dating from the period of the later Ptolemies and of the Roman emperors Augustus and Tiberius (30 BC–AD 37), were, however, never completed. The Roman emperor Hadrian (reigned AD 117–138) added a gate west of the complex. Other small temples or shrines dedicated to Egyptian deities include a temple to Imhotep and one to Hathor, as well as chapels to Osiris, Horus, and Nephthys.

The Temple of Isis continued to flourish during Roman times and was not closed until the reign of Justinian I (AD 527–565). Late in Justinian's reign the temple was converted into a church, and two other Coptic churches were built in the still-prosperous town.

All these structures were thoroughly explored and reinforced (1895–96) before being partially flooded behind the old Aswan Dam. In 1907 a careful inspection revealed that salts in the water were harming paints on the decorations. When the temples reemerged after 1970 with the completion of the High Dam (Aswan High Dam) upstream, it was found that considerable damage had been done to the shrines. A decision was therefore made to remove them to higher ground on the nearby island of Agilkia. The island was leveled to resemble the original Philae, and the temples were rebuilt, restoring to them some measure of their original beauty prior to their formal reopening in 1980.